Comparison between the types for the ages and genders

Questions

  • What are the differences between the type for the different combinations of ages and genders?
  • Do we observe the same changes as globally?

Loads

Libraries and functions

Warning message in is.na(x[[i]]):
“is.na() applied to non-(list or vector) of type 'environment'”
==========================================================================
*
*  Package WGCNA 1.63 loaded.
*
*    Important note: It appears that your system supports multi-threading,
*    but it is not enabled within WGCNA in R. 
*    To allow multi-threading within WGCNA with all available cores, use 
*
*          allowWGCNAThreads()
*
*    within R. Use disableWGCNAThreads() to disable threading if necessary.
*    Alternatively, set the following environment variable on your system:
*
*          ALLOW_WGCNA_THREADS=<number_of_processors>
*
*    for example 
*
*          ALLOW_WGCNA_THREADS=4
*
*    To set the environment variable in linux bash shell, type 
*
*           export ALLOW_WGCNA_THREADS=4
*
*     before running R. Other operating systems or shells will
*     have a similar command to achieve the same aim.
*
==========================================================================


Allowing multi-threading with up to 4 threads.
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."
[1] "preparing gene to GO mapping data..."
[1] "preparing IC data..."

Data

Stats

Wald padj < 0.05LFC > 0 (Wald padj < 0.05)LFC < 0 (Wald padj < 0.05)
GF VS SPF (F, 8w) 392192 200
GF VS SPF (M, 8w) 161 76 85
GF VS SPF (F, 52w) 738316 422
GF VS SPF (M, 52w) 393145 248
GF VS SPF (F, 104w)2038846 1192
GF VS SPF (M, 104w)2172898 1274

Differentially expressed genes

Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages):
“argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G):
“initial point very close to some inequality constraints”

Comparison of the numbers per ages

Differentially expressed genes

DEG into gene co-expression network

  • White: up-regulated
  • Black: down-regulated
GF vs SPF 8w 52w 104w
F
M

GO analysis

Biological process

Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)

Network based on description similarity

GF vs SPF 8w 52w 104w
F
M

GF VS SPF (F, 8w)

<!DOCTYPE html>

GF VS SPF (M, 8w)

<!DOCTYPE html>

GF VS SPF (F, 52w)

<!DOCTYPE html>

GF VS SPF (M, 52w)

<!DOCTYPE html>

GF VS SPF (F, 104w)

<!DOCTYPE html>

GF VS SPF (M, 104w)

<!DOCTYPE html>

Cellular components

Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 6 rows containing missing values (geom_point).”

Molecular functions

Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)

Warning message:
“Removed 6 rows containing missing values (geom_point).”

KEGG pathways

[1] "Note: 39 of 3451 unique input IDs unmapped."
[1] "Note: 39 of 3451 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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“Calling 'structure(NULL, *)' 
limit_output extension: Maximum message size of 10000 exceeded with 10090 characters

Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/

[1] "Note: 39 of 3451 unique input IDs unmapped."
Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”Warning message in structure(x$children, class = "XMLNodeList"):
“Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.”

Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/

Comparison with Erny results

Protocol: 2 months old female mices (GF vs SPF)

Raw comparison of the results

SymbolsGenesfold.d.hGF_1GF_2GF_3GF_4GF_5GF_7GF_8SPF_1SPF_2SPF_3SPF_4SPF_6SPF_7SPF_8t.test
Ddit4 NM_029083 3.488386 232 420 140 116 1027 785 501 40 21 22 13 73 70 48 0.007198903
Iqgap1 NM_016721 2.545650 24 44 10 16 20 17 50 4 14 2 3 1 6 1 0.003764139
Tsc22d3 NM_0010773642.416164 47 107 44 53 257 214 132 23 17 23 20 39 16 22 0.009737505
Rab3d NM_031874 2.369234 7 14 5 10 2 7 17 1 1 1 1 3 1 4 0.004171454
Gnaz NM_010311 2.280108 1 1 5 5 9 9 4 1 1 1 1 1 1 1 0.009123198
Agpat4 NM_026644 1.984893 5 21 21 10 15 10 13 4 7 1 1 5 5 1 0.001279054
1700037C18Rik
-0.726653411890693
Lrmda
-3.64638532054075
Tcim
1.05252272836875
Ccdc191
-1.07325728126671
2610524H06Rik
1.32511199395419
6330407A03Rik
-1.99177874144356
ernyour
Ddit4 3.4883860 3.6294025
Tsc22d3 2.4161642 1.4193018
Notch4 1.4226911 1.6315226
Sult1a1 1.2561528 1.1617315
Capg 0.9126729 0.5168264
Ucp2 0.9111967 0.5044607
Gpr137b 0.8032544 1.2266600
Pnpla2 0.7100179 0.4259134
Ogfrl1 0.6877922 0.6959325
Arhgef6-1.0246621 0.4253851
Gpr137b-ps-1.1178365-3.0251734
Upk1b-1.1300605-0.6517569
Cntrl-1.3303078-0.9347969
Apobec2-1.4288433-0.8472098
Ly86-1.4389640-0.9562232
Stard3nl-1.4780473-0.4310033
Fkbp7-1.6261852-0.3942576
Malat1-1.7120031-1.1023659
Mcur1-1.7424200-0.8593199
Nos1ap-1.8022360-0.8171791
Zfp318-1.8961642-0.7895965
Lrba-2.0198996-0.6372855
Far1-2.5766472 0.5588240
Ero1lb-3.2172307-1.3952799

Detailed comparison

  • Checking the correlation between the counts of Erny and our counts
  • Re-running a DGE analysis on the Erny's raw counts
Error in counts[, SPF_F_8w_samples]: object of type 'closure' is not subsettable
Traceback: